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(-) Description

Title :  GPPNHP-BOUND RAB33 GTPASE
 
Authors :  S. Eathiraj, X. Pan, C. Ritacco, D. G. Lambright
Date :  01 Mar 05  (Deposition) - 26 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  A
Keywords :  Rab Gtpase, Rab33B Gtpase, Vesicular Trafficking, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Eathiraj, X. Pan, C. Ritacco, D. G. Lambright
Structural Basis Of Family-Wide Rab Gtpase Recognition By Rabenosyn-5.
Nature V. 436 415 2005
PubMed-ID: 16034420  |  Reference-DOI: 10.1038/NATURE03798
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN RAB-33B
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidMODIFIED PET15B
    Expression System StrainBL21 (DE3) CODON PLUS-RIL CELLS
    Expression System Taxid562
    Expression System Vector Type6XHIS FUSION, PET VECTOR
    GeneRAB33B
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:47 , THR A:65 , GNP A:204 , HOH A:210 , HOH A:218BINDING SITE FOR RESIDUE MG A 203
2AC2SOFTWARESER A:42 , ASN A:43 , VAL A:44 , GLY A:45 , LYS A:46 , THR A:47 , CYS A:48 , PHE A:58 , THR A:62 , ALA A:64 , THR A:65 , GLY A:91 , ASN A:148 , LYS A:149 , ASP A:151 , LEU A:152 , SER A:178 , ALA A:179 , LYS A:180 , MG A:203 , HOH A:210 , HOH A:215 , HOH A:218 , HOH A:227 , HOH A:258 , HOH A:272 , HOH A:285BINDING SITE FOR RESIDUE GNP A 204

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z06)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Z06)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z06)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z06)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z06)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:165
 aligned with RB33B_MOUSE | O35963 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:165
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191     
          RB33B_MOUSE    32 RIFKIIVIGDSNVGKTCLTYRFCAGRFPDRTEATIGVDFRERAVDIDGERIKIQLWDTAGQERFRKSMVQHYYRNVHAVVFVYDMTNMASFHSLPAWIEECKQHLLANDIPRILVGNKCDLRSAIQVPTDLAQKFADTHSMPLFETSAKNPNDNDHVEAIFMTLA 196
               SCOP domains d1z06a1 A:32-196 Rab-33b                                                                                                                                              SCOP domains
               CATH domains 1z06A00 A:32-196 P-loop containing nucleotide triphosphate hydrolases                                                                                                 CATH domains
               Pfam domains ---Ras-1z06A01 A:35-196                                                                                                                                               Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhh.............eeeeeeee..eeeeeeeee...hhhhhh.hhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh......eeeeee...hhhhh..hhhhhhhhhhhh...eee....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z06 A  32 RIFKIIVIGDSNVGKTCLTYRFCAGRFPDRTEATIGVDFRERAVDIDGERIKIQLWDTAGQERFRKSMVQHYYRNVHAVVFVYDMTNMASFHSLPAWIEECKQHLLANDIPRILVGNKCDLRSAIQVPTDLAQKFADTHSMPLFETSAKNPNDNDHVEAIFMTLA 196
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191     

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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Family: Ras (176)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RB33B_MOUSE | O35963)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    GO:0006891    intra-Golgi vesicle-mediated transport    The directed movement of substances within the Golgi, mediated by small transport vesicles. These either fuse with the cis-Golgi or with each other to form the membrane stacks known as the cis-Golgi reticulum (network).
    GO:1903434    negative regulation of constitutive secretory pathway    Any process that stops, prevents or reduces the frequency, rate or extent of constitutive secretory pathway.
    GO:0000042    protein targeting to Golgi    The process of directing proteins towards the Golgi; usually uses signals contained within the protein.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:1903358    regulation of Golgi organization    Any process that modulates the frequency, rate or extent of Golgi organization.
    GO:2000785    regulation of autophagosome assembly    Any process that modulates the frequency, rate or extent of autophagosome assembly.
    GO:2000156    regulation of retrograde vesicle-mediated transport, Golgi to ER    Any process that modulates the frequency, rate or extent of retrograde vesicle-mediated transport, Golgi to ER.
    GO:0048705    skeletal system morphogenesis    The process in which the anatomical structures of the skeleton are generated and organized.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005796    Golgi lumen    The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RB33B_MOUSE | O359632g77

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